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Regarding things like dockers and flatpaks, I mostly "solve" it by only running official images, or at least images from the same dev as the program, where possible.
But also IMO there's little to no reason to fear when using things like flatpaks. Most exploits one hears of nowadays are of the kind "your attacker needs to get a shell into your machine in the first place" or in some cases evn "your attacker needs to connect to an instance of a specific program you are running, with a specific config", so if you apply any decent opsec that's already a v high barrier of entry.
And speaking of Debian, that does bring to mind the one beef I have with their packaging system: that when installing a package it starts the related services by default, without even giving you time to configure them.